FW: [Cytoscape-discuss] Analyzing large networks in Cytoscape

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Barry Demchak

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Jul 15, 2016, 11:51:52 AM7/15/16
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From: cytoscap...@googlegroups.com [mailto:cytoscap...@googlegroups.com] On Behalf Of Neels
Sent: Friday, July 15, 2016 4:03 AM
To: cytoscape-discuss
Subject: Re: [Cytoscape-discuss] Analyzing large networks in Cytoscape

 

@Scooter Morris 

Hi. I am using Cytoscape 3.4 on a Dell Tower workstation with 256 GB RAM. My cytoscape.vmoptions file shows 

-Xms2048M

-Xmx248690M means 248.69 GB heap memory.

Now, I am stuck at the merge network option for almost 24 hours. I really need to do this since I have to create a large network for my organism of interest as it is not present in Cytoscape. Any suggestions?? 


On Wednesday, February 18, 2015 at 10:44:19 PM UTC+5:30, Scooter Morris wrote:

Hi Matthias,
    I often work with networks of that size (or much larger).  On the other hand, the Cytoscape "merge networks" function can be extremely slow.  I would suggest downloading a single interactome (there are several sample ones on the startup screen) and avoiding the merge step.  Cytoscape also gets really memory hungry for large networks, so you should watch the little memory icon in the lower right hand corner to tell you if you are running out of memory.

-- scooter

On 02/18/2015 06:13 AM, Mat wrote:

Hello everyone,

 

I'm a beginner in Cytoscape and I want to use it for analyzing RNA seq data, by applying for example ClueGO and BinGO.

 

I had the idea that I could make very large protein interaction networks and subsequently load my data files onto it.

So I imported and merged the interactomes that could be downloaded by the Web Service Client (I forgot the number of nodes but about 600k edges) and loaded a data file and tried to do some analyses using these apps.

 

This failed however in that it got stuck at 'finalizing' for more than 24 hours. 

 

I'm using Cytoscape 3.2.0 and the specs of the (Windows 7 64-bit) pc are:

12 Gb Ram

Intel XEON X5650 @ 2.67 GHz

ATI FireMV 2260

Java 8 v31

 

So I have a few questions that I hope to see answered. 

Are these networks to big for Cytoscape to handle or are my specs just not good enough? and if the latter is the case, what specs should then work?

Finally, is the OS X or Linux version of Cytoscape better able to handle large datasets?

 

Regards,

 

Matthias

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Alexander Pico

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Jul 21, 2016, 1:13:12 PM7/21/16
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Hi Matthias,

If the merge function is still taking too long, even giving it all your RAM, then I think Scooter's other suggestion is the only way to go...  Combine your source files prior to importing into Cytoscape. If they are the same data type, then a simple concatentation will work. Cytoscape will handle redundant node and interactions upon import, no problem.

 - Alex

On Friday, July 15, 2016 at 8:51:52 AM UTC-7, Barry Demchak wrote:

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